Description of the data and file structure

These files comprise the raw data for the paper “CRISPRi-mediated repression of three cI repressors induces the expression of three related Neisseria gonorrhoeae bacteriophages” published in the Journal of Bacteriology in May 2025. We have submitted our raw CFU/mL Liquid Death curve counts for each CRISPRi-carrying N. gonorrhoeae strain with a ngo0479, ngo1116, or ngo1630-targeting spacer treated with or without IPTG (CRISPRi-NGO0479_Liquid_Death_Curve.xlsx, CRISPRi-NGO1116_Liquid_Death_Curve.xlsx, CRISPRi-NGO1630_Liquid_Death_Curve.xlsx), raw RNA-sequencing data from the CRISPRi-NGO0479, CRIPSRI-NGO1116, and CRISPRi-NGO1630 strains following bacterial liquid growth, supplemented with or without IPTG (Raw CRISPRi_RNA-sequencing_Raw_data.xlsx), folder containing raw Transmission Electron Microscopy images labeled according to the figure each image corresponds with in the paper (TEM_Raw_Images.zip), measurements of phage heads released following growth with or without IPTG for the CRISPRi-NGO0479, CRISPRi-NGO1116, and CRISPRi-NGO1630 strains (Phage_Head_Measurements.xlsx), measurements of phage tails released following growth with IPTG for the CRISPRi-NGO0479, CRISPRi-NGO1116, and CRISPRi-NGO1630 strains (Phage_Tail_Measurements-1.xlsx). A copy of the README is included in RTF format (README.rtf).

CRISPRi-NGO0479_Liquid_Death_Curve.xlsx, CRISPRi-NGO1116_Liquid_Death_Curve.xlsx, CRISPRi-NGO1630_Liquid_Death_Curve.xlsx

• These are 3 separate files, each file representing the strain which it is named after
  • Hours = How long the bacteria were grown in liquid culture before isolating samples to perform CFU/mL dilutions and calculations
  • 1 mM or 0 mM IPTG = The concentration of IPTG added to the liquid culture at the start of the experiment
  • Data represent 3 biological replicates with 9 technical replicates per condition and time point
  • CFU/mL = data represented as “Colony Forming Units per milliliter”

Raw CRISPRi_RNA-sequencing_Raw_Data.xlsx

• Tabs
  • NGO0479 0 mM vs 1 mM IPTG = N. gonorrhoeae CRISPRi-NGO0479 strain grown with and without IPTG; RNA was isolated and sequenced. This tab shows the RNA transcript abundance for every gene in the bacteria
  • NGO0479 Significant Genes = this tab contains the transcript abundance for the genes that displayed significant differences in RNA transcript abundance between 0 and 1 mM IPTG
  • NGO1116 0 mM vs 1 mM IPTG = N. gonorrhoeae CRISPRi-NGO1116 strain grown with and without IPTG; RNA was isolated and sequenced. This tab shows the RNA transcript abundance for every gene in the bacteria
  • NGO1116 Significant Genes = this tab contains the transcript abundance for the genes that displayed significant differences in RNA transcript abundance between 0 and 1 mM IPTG
  • NGO1630 0 mM vs 1 mM IPTG = N. gonorrhoeae CRISPRi-NGO1630 strain grown with and without IPTG; RNA was isolated and sequenced. This tab shows the RNA transcript abundance for every gene in the bacteria
  • NGO1630 Significant Genes = this tab contains the transcript abundance for the genes that displayed significant differences in RNA transcript abundance between 0 and 1 mM IPTG
• Columns:
  • Locustag = refers to the locus in which the gene corresponds in the N. gonorrhoeae N-1-60 strain
  • Gene = 4-letter name for gene; if the gene did not have a name, “N/A” is written
  • Feature Type = feature in the genome; CDS = coding sequencee
  • Pvalue = P-value of the difference in transcript abundance
  • Benjamini_Hochberg_Adjusted_PValue = Benjamini-Hochberg P-value Adjustment
  • (0479, 1116, or 1630 1mM_2 hr) = RNA transcript abundance for each strain following growth in liquid media supplemented with 1 mM IPTG for 2 hours
  • (0479, 1116, or 1630 0mM_2 hr) = RNA transcript abundance for each strain following growth in liquid media supplemented with 0 mM IPTG for 2 hours

TEM_Raw_Images.zip

• This folder contains the RAW TEM (Transmission Electron Microscopy) tif images used for the paper. The name of each file corresponds to the figure in which the image was used for the paper. The number value indicates which image in the Figure row it corresponds to (from left to right, 1 to 3 [if a row contains 3 images] or 1 to 2 [if a row contains 2 images])
• In each image, the bottom of the image is a scale
  • “nm” = nanometer

Phage_Head_Measurements.xlsx

• This file contains the head diameter measurements of phage — or non-phage vesicles — isolated from the CRISPRi-NGO0479, CRISPRi-NGO1116, and CRISPRi-NGO1630 strains grown with or without IPTG
• Measurements were acquired by analyzing TEM images with ImageJ
• Each cell represents a single phage head or vesicle
• All values are nanometer (“nm”) measurements
• Tabs:
  • 1 mM IPTG CRISPRi-ngo0479 (nm) = phage particle head measurements (in nanometers) from CRISPRi-NGO0479 strain grown with 1 mM IPTG
  • 0 mM IPTG CRISPRi-ngo0479 (nm) = vesicle measurements (in nanometers) from CRISPRi-NGO0479 strain grown with 0 mM IPTG
  • 1 mM IPTG CRISPRi-ngo1116 (nm) = phage particle head measurements (in nanometers) from CRISPRi-NGO1116 strain grown with 1 mM IPTG
  • 0 mM IPTG CRISPRi-ngo1116 (nm) = vesicle measurements (in nanometers) from CRISPRi-NGO1116 strain grown with 0 mM IPTG
  • 1 mM IPTG CRISPRi-ngo1630 (nm) = phage particle head measurements (in nanometers) from CRISPRi-ngo1630 strain grown with 1 mM IPTG
  • 0 mM IPTG CRISPRi-ngo1630 (nm) = vesicle measurements (in nanometers) from CRISPRi-NGO1630 strain grown with 0 mM IPTG

Phage_Tail_Measurements-1.xlsx

• This file contains the tail lengths measurements of phage isolated from the CRISPRi-NGO0479, CRISPRi-NGO1116, and CRISPRi-NGO1630 strains grown with IPTG
  • All measurements are in nanometers (“nm”); each cell represents a single tail
  • Measurements were made through ImageJ analysis of TEM images
• Tabs:
  • Cummulative = the lengths of all tails measured from the CRISPRi-NGO0479, CRISPRi-NGO1116, and CRISPRi-NGO1630 strains, combined in a single list
  • CRISPRi-NGO0479 +IPTG (nm) = the lengths of tails measured from the CRISPRi-NGO0479 strain following growth with 1 mM IPTG; nm = nanometers
  • CRISPRi-NGO1116 +IPTG (nm) = the lengths of tails measured from the CRISPRi-NGO1116 strain following growth with 1 mM IPTG; nm = nanometers
  • CRISPRi-NGO1630 +IPTG (nm) = the lengths of tails measured from the CRISPRi-NGO1630 strain following growth with 1 mM IPTG; nm = nanometers